Research workbench
Cryo-EM structure of ntd-directed neutralizing antibody 5-24 in complex with prefusion SARS-cov-2 spike glycoprotein
Analyse Cryo-EM structure of ntd-directed neutralizing antibody 5-24 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L2F
- Type
- protein
- Length
- 3,970 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; 5-24 heavy chain; 5-24 light chain
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 20% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Spike glycoprotein | protein | 1088 | 21% helix, 31% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1089 | 23% helix, 31% strand | P0DTC2 |
| H, G, I | 5-24 heavy chain | protein | 126 | 4% helix, 39% strand | — |
| L, J, K | 5-24 light chain | protein | 109 | 3% helix, 43% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 72 copies · chains A, C, B, H, I, G
- BMA · beta-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.85 | 0.90 | 99 | empty |
| 2 | 817 | 0.83 | 0.86 | 104 | empty |
| 3 | 324 | 0.83 | 0.92 | 31 | empty |
| 4 | 332 | 0.79 | 0.90 | 53 | empty |
| 5 | 313 | 0.77 | 0.89 | 50 | empty |
Interfaces
12 interfaces between chains.
- B–C · 6629 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 6570 Ų buried · 61 hydrogen bonds · protein-protein
- A–C · 6560 Ų buried · 62 hydrogen bonds · protein-protein
- I–K · 1024 Ų buried · 5 hydrogen bonds · protein-protein
- H–L · 1022 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 glycan, 48 disulfide (N-glycosylation, disulfide).
Compared structures
- 7L2F · Cryo-EM structure of NTD-directed neutralizing antibody 5-24 in complex with prefusion… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 7L2F · PDBe 7L2F · UniProt P0DTC2
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